Journal Of Applied Genetics[JOURNAL]
Sun
200 papers
miRNA-mRNA network analysis reveals novel post-transcriptional regulators and therapeutic targets in coronary artery disease.
Paul P, Sahoo OS, Narang R … +6 more , Badal AK, Nayek A, Dhar R, Mukherjee O, Yadav S, Karmakar S
J Appl Genet · 2026 May · PMID 42162444 · Publisher ↗
Coronary artery disease (CAD) remains one of the leading causes of mortality worldwide, driven by complex gene regulatory mechanisms. Non coding RNAs such as microRNAs (miRNAs) act as pivotal regulators of CAD pathogenes...
Coronary artery disease (CAD) remains one of the leading causes of mortality worldwide, driven by complex gene regulatory mechanisms. Non coding RNAs such as microRNAs (miRNAs) act as pivotal regulators of CAD pathogenesis. This study employed a multi-omics in silico approach to uncover microRNA (miRNA)-mediated regulatory networks in CAD. Differentially expressed miRNAs were identified from patient cohorts and mapped to target genes. Overlapping common genes (OCGs) between predicted targets and CAD-associated DEGs were used to construct a regulatory network. Hub miRNAs were prioritized, identifying 20 key regulators, including 11 novel hub-level regulatory candidates not previously prioritized as master regulators in integrated CAD miRNA network analyses. Functional enrichment confirmed the involvement of these OCGs in atherosclerosis and cardiomyopathy. A competing endogenous miRNA-lncRNA network was built to explore multi-layered regulation. Possible drug targets were analyzed to assess therapeutic potential for the results. This integrative pipeline offers insights into miRNA-driven CAD mechanisms and highlights novel biomarkers and targets for clinical implementation.
The transcription factor LEC2 as an epigenetic regulator of plant totipotency: from Arabidopsis to crop improvement.
Gaj MD
J Appl Genet · 2026 May · PMID 42151653 · Publisher ↗
Plant cell totipotency-the ability of a differentiated somatic cell to regenerate a complete organism-is one of the most remarkable features of plant development and a cornerstone of biotechnology. Somatic embryogenesis...
Plant cell totipotency-the ability of a differentiated somatic cell to regenerate a complete organism-is one of the most remarkable features of plant development and a cornerstone of biotechnology. Somatic embryogenesis (SE) represents the most striking manifestation of this potential, serving as a powerful system for clonal propagation, genetic transformation, and functional genomics. At the molecular level, SE is governed by transcription factors (TFs) that integrate hormonal and metabolic signals with chromatin remodeling to activate embryogenic programs in somatic cells. Among SE-related TFs, LEAFY COTYLEDON2 (LEC2) of Arabidopsis thaliana has emerged as an essential regulator of embryogenic transition. LEC2 functions both as an auxin-responsive developmental switch and as an epigenetic modulator that recruits chromatin regulators to reprogram transcriptional networks controlling the totipotency of plant cells. This review (i) outlines the utility of Arabidopsis as a model for studying SE and totipotency, (ii) highlights the dual role of LEC2 as both a target and an architect of epigenetic regulation, and (iii) explores translational perspectives for TF-based strategies in plant regeneration and crop improvement. The evidence demonstrating that LEC2 coordinates transcriptional regulation with epigenetic remodeling, acting as a central hub of plant totipotency, is summarized and illustrated graphically. LEC2-centered insights into SE not only deepen our understanding of the molecular basis of plant totipotency but also provide a conceptual framework for improving regeneration efficiency across plant species.
Phytocannabinoids as epigenetic regulators: bridging DNA methylation and redox homeostasis in glioblastoma.
Barciszewska AM, Belter A, Barciszewski JF … +4 more , Bartkowski L, Giel-Pietraszuk M, Gawrońska I, Naskręt-Barciszewska MZ
J Appl Genet · 2026 May · PMID 42118523 · Publisher ↗
Glioblastoma, a primary brain tumor of the CNS, is the most malignant lesion among gliomas. It has a median survival time of about 12-15 months after diagnosis and limited treatment options. That neoplastic processes res...
Glioblastoma, a primary brain tumor of the CNS, is the most malignant lesion among gliomas. It has a median survival time of about 12-15 months after diagnosis and limited treatment options. That neoplastic processes result from changes in the cell's redox potential and the overproduction of reactive oxygen species. As a consequence, the epigenetic marker, mC of DNA, is oxidized with ROS to 5-hydroxymethylcytosine, but guanosine is damaged to 8-oxo-dG, a general probe of oxidative stress. If so, the mC, as well as 8-oxo-dG content in DNA, are subject to dynamic changes induced by environmental and endogenous cellular factors. These markers can be used to evaluate new therapeutic agents, among others. Currently, there are no effective drugs against human glioblastoma. Cannabinoids, small, lipophilic molecular compounds, are increasingly being studied for their antitumor properties. Using the precise nucleotide post-labelling method and thin-layer chromatographic analysis we monitored the effect of CBD, THC, and CFE, as well as their combination with temozolomide, on changes of global mC and 8-oxo-dG contents. These results show that cannabinoids alone or in combination with the current standard glioblastoma chemotherapeutic, TMZ, inhibit the progression of GBM and could be used for its clinical treatment. The mechanism of cannabinoids' actions on glioblastoma cells is also proposed.
Genetic analysis and reproductive interventions in families affected by congenital cataracts: a study of 107 cases.
Li YH, Wang Q, Peng Y … +11 more , Du J, Hu L, Tan ZH, Gu F, Hu H, Zhang QJ, Lin G, Lu GX, Tan YQ, Zhou L, He WB
J Appl Genet · 2026 May · PMID 42118522 · Publisher ↗
Congenital cataract is a vision impairment that arises before birth or within the first year of life due to lens opacity, with genetic disorders being a significant contributing factor. The purpose of this study is to id...
Congenital cataract is a vision impairment that arises before birth or within the first year of life due to lens opacity, with genetic disorders being a significant contributing factor. The purpose of this study is to identify the pathogenic variants associated with congenital cataract to inform clinical diagnosis, treatment, reproductive intervention. Next-generation sequencing was performed on 107 families with congenital cataracts, followed by Sanger sequencing validation and familial analysis of candidate variants. RNA splicing pattern analysis was conducted on variants located near splicing sites. A total of 44 likely pathogenic or pathogenic variants (including 20 novel variants) in 46 families, and 19 variants of uncertain significance (VUS) in 19 families were identified, with a detection rate of 43.0%. A total of 14 VUS were sub-classified as "warm" or "hot" VUS based on Bayesian analysis. PGT or prenatal diagnosis was conducted in 26 families; follow-up revealed that 16 families opted for PGT and successfully delivered 10 healthy children. Among 10 families that pursued prenatal diagnosis after natural conception, 8 gave birth to healthy children.This study expanded the variant spectrum and providing valuable insights for the prevention and management of this condition.
Beyond the complex: inosine drives the antiviral and epigenetic effects of inosine pranobex.
Wawrzyniak D, Dutkiewicz M, Dorna D … +8 more , Kątny M, Naskręt-Barciszewska M, Głodowicz P, Pieczuro J, Rolle K, Idczak Ł, Romankiewicz S, Barciszewski J
J Appl Genet · 2026 May · PMID 42104047 · Publisher ↗
Inosine pranobex (IP) is a long-used antiviral drug whose mechanism of action remains incompletely understood. However, molecular efficacy has been attributed mainly to immunomodulatory effects. There are data which sugg...
Inosine pranobex (IP) is a long-used antiviral drug whose mechanism of action remains incompletely understood. However, molecular efficacy has been attributed mainly to immunomodulatory effects. There are data which suggest that the cellular activity of IP stems from its major constituent compound, inosine, known for its pleiotropic roles in purine metabolism, RNA modification, and translation regulation. We investigated whether IP acts as a stable complex or a mixture of its components and compared the biological effects of inosine itself and IP in vitro. The structural composition of IP was analyzed using compositional and microscopic methods. Cytotoxicity, antiviral activity against coxsackievirus B3 (CVB-3), and global DNA methylation changes were evaluated in A549 and HeLa cell lines using MTT, colony formation, plaque reduction, and post-labeling methods, respectively. We found that IP is physically heterogeneous and function as a mixture of components rather than a stable complex. In cell-based assays, inosine exhibited higher antiviral activity than IP, particularly under pre-treatment conditions, where it provided stronger protection against CVB-3-induced cytopathic effects. Neither compound showed significant cytotoxicity within the tested concentration ranges. Both inosine and IP influenced global DNA methylation levels, but inosine induced more pronounced and concentration-dependent changes. The superior antiviral and epigenetic activity of inosine compared with IP suggests that inosine is the main principal active component responsible for IP's biological effects. While IP's immunomodulatory functions were not evaluated here, our findings strongly suggest that inosine contributes substantially to its antiviral efficacy. Further studies, including in vivo models, are warranted to clarify the epigenetic mechanism underlying these observations.
Correction to: Molecular interplay of lncRNAs, miRNAs, and mRNAs axes in triple-negative breast cancer: implications for metastatic progression.
Rathore D, Agarwal I, Patel S … +4 more , Adnani N, Dharwal N, Shukla N, Dave HV
J Appl Genet · 2026 May · PMID 42095949 · Publisher ↗
Abstract loading — click title to view on PubMed.
Novel SCN5A variant associated with flecainide-responsive multifocal ventricular arrhythmia and recovered cardiomyopathy.
Biernacka EK, Ponińska J, Smarż K … +1 more , Budaj A
J Appl Genet · 2026 May · PMID 42087028 · Publisher ↗
Multifocal Ectopic Purkinje-related Premature Contractions (MEPPC) is a rare genetic arrhythmogenic syndrome caused by gain-of-function mutations in the SCN5A gene, leading to frequent multifocal premature ventricular co...
Multifocal Ectopic Purkinje-related Premature Contractions (MEPPC) is a rare genetic arrhythmogenic syndrome caused by gain-of-function mutations in the SCN5A gene, leading to frequent multifocal premature ventricular contractions and risk of cardiomyopathy. We report a case highlighting the diagnostic and therapeutic challenges associated with unrecognized MEPPC. A 27-year-old woman presented with highly symptomatic ventricular and supraventricular arrhythmias and severe left ventricular dysfunction, refractory to conventional therapy and ablation. Initiation of flecainide resulted in immediate arrhythmia suppression and full recovery of cardiac function. Genetic testing revealed two SCN5A variants: a novel likely pathogenic p.(Val215Ala) located in a known MEPPC hotspot, and p.(Phe1570Cys), a variant with known loss-of-function properties, unlikely to be causative in MEPPC but potentially modulating the phenotype. This report underscores the importance of early recognition of MEPPC based on arrhythmic patterns and the critical role of targeted genetic testing in optimizing treatment strategies.
Transformative Applications and Innovations in Next-Generation Sequencing Data Analysis.
Beura A, Dakal TC, Rajguru MS … +3 more , Manjunath GK, Mahalingam S, Kumar A
J Appl Genet · 2026 May · PMID 42068517 · Publisher ↗
Next-generation sequencing (NGS) has revolutionized the field of genomics by providing rapid, high-throughput, and cost-effective platforms for analyzing genomes, transcriptomes, and epigenomes. Its application spans can...
Next-generation sequencing (NGS) has revolutionized the field of genomics by providing rapid, high-throughput, and cost-effective platforms for analyzing genomes, transcriptomes, and epigenomes. Its application spans cancer genomics, infectious disease research, rare disease diagnostics, and precision medicine, enabling comprehensive detection of genetic variants and their functional implications. The advent of advanced methods such as single-cell sequencing, long-read technologies, and multi-omics integration has further expanded the scope of NGS, allowing unprecedented insights into cellular heterogeneity, structural variations, and systems-level interactions. These innovations have facilitated the identification of actionable mutations, supported biomarker discovery, and enhanced our understanding of complex biological processes in both research and clinical contexts. Despite these advancements, several challenges remain. The vast volume of sequencing data necessitates robust computational infrastructures for storage, processing, and interpretation. Sequencing error rates, though improving, continue to impact variant detection and clinical reliability. Ethical concerns regarding privacy, data sharing, and equitable access are also critical barriers that must be addressed, particularly in resource-limited settings. Moreover, translating genomic findings into clinically actionable outcomes requires standardized frameworks and interdisciplinary collaboration among clinicians, geneticists, and bioinformaticians. Looking ahead, the integration of artificial intelligence, machine learning, and automation into NGS data pipelines promises to significantly enhance accuracy, scalability, and clinical utility. These emerging innovations, coupled with global efforts to ensure accessibility and ethical implementation, position NGS as a cornerstone of precision medicine, paving the way for individualized treatment strategies and transformative improvements in healthcare delivery.
Horse racing towards antibiotic resistance. Accompanying animals as a source of antibiotic-resistant bacteria.
Lepianka A, Sitkiewicz I
J Appl Genet · 2026 Apr · PMID 42050107 · Publisher ↗
Antibiotic resistance is a significant issue in modern infectious medicine and veterinary science, with animals, including horses, playing a crucial role in its dissemination. Antibiotics, used both for treatment and pre...
Antibiotic resistance is a significant issue in modern infectious medicine and veterinary science, with animals, including horses, playing a crucial role in its dissemination. Antibiotics, used both for treatment and prevention of diseases in animals, influence the composition of the microbiota and promote the selection of resistant strains that can be transmitted to humans through direct or environmental contact. Horses, currently classified as companion animals, serve as a reservoir of commensal and pathogenic bacteria, including multidrug-resistant strains capable of horizontal gene transfer. Of particular importance are plasmids and integrons that carry genes encoding β-lactamases, which significantly reduce the effectiveness of therapy in both humans and animals. Analysis of the equine oral and gut microbiota highlights the potential of these environments as sources and vectors of resistance. Understanding the mechanisms underlying the transfer and persistence of resistance genes in horses is crucial for public health and helps define new directions for research within the One Health framework.
Local estrogen therapy effects on DNA methylation dynamics in menopausal women-a cross-sectional preliminary study.
Szymański JK, Malinowska M, Jakiel G … +3 more , Słabuszewska-Jóźwiak A, Scholz A, Jakóbkiewicz-Banecka J
J Appl Genet · 2026 Apr · PMID 42036589 · Publisher ↗
Postmenopause is characterized by a permanent decline in estrogen levels, effecting various tissues and contributing to systemic aging. Reduced hormonal levels negatively impact vaginal health, leading to tissue atrophy,...
Postmenopause is characterized by a permanent decline in estrogen levels, effecting various tissues and contributing to systemic aging. Reduced hormonal levels negatively impact vaginal health, leading to tissue atrophy, which can be alleviated with topical estrogen therapies. This study aimed to assess the effects of menopausal hormone deficiencies on DNA methylation in vaginal tissue and swabs, compared to buccal swabs, and evaluate the impact of local estrogen therapy on these changes. Samples from 126 women were categorized into three groups: premenopausal, postmenopausal without local estrogen therapy, and postmenopausal with local estrogen therapy. Postmenopausal women with urogenital atrophy exhibited elevated cytosine methylation (5-mC) compared to premenopausal women, whereas those receiving local estrogen therapy had 5-mC levels similar to premenopausal women. Additionally, 5-hydroxymethylcytosine (5-hmC) levels, a marker of demethylation, was also higher in the estrogen-treated group. The 5-mC/5-hmC ratio was notably elevated in women with urogenital atrophy. Significant differences in DNA methylation dynamics were observed in vaginal samples but not in buccal swabs among postmenopausal groups. Menopausal hormonal deficiencies lead to epigenetic changes in vaginal tissue, particularly increased cytosine methylation. Local estrogen therapy can mitigate these changes, providing insights into aging processes. Analyzing DNA methylation in vaginal swabs may serve as a non-invasive tool for monitoring age-related changes and assessing therapeutic efficacy. Further research is needed to understand these epigenetic modifications and their clinical implications.
Artificial intelligence in neurofibromatosis type I: diagnostic and therapeutic opportunities.
Błaszkiewicz J, Madej-Pilarczyk A, Ciara E
J Appl Genet · 2026 Apr · PMID 42032418 · Publisher ↗
The dynamic growth in the use of artificial intelligence (AI) in medicine is driven by advances in computer processing power, memory, and data storage capabilities. The digital progress, combined with continuously growin...
The dynamic growth in the use of artificial intelligence (AI) in medicine is driven by advances in computer processing power, memory, and data storage capabilities. The digital progress, combined with continuously growing datasets, enables the development of modern tools that support oncological, neurological, and genetic diagnostics. Achievements in the application of AI in medicine make it possible to analyze genotype–phenotype correlations, and rare diseases, which include more than 6,000 distinct conditions characterized by unique phenotypes and complex pathomechanisms, present a particular challenge in this context. This article presents the basic issues related to machine learning and describes the mechanisms of the most commonly used algorithms. In addition, a review was conducted of modern tools that enable the analysis of genotype–phenotype correlations and the prediction of symptoms of the rare disease neurofibromatosis type 1 (NF1). Tools developed so far to support therapeutic decision-making related to NF1 were collected and described. The tools were classified according to their functionality, and their usefulness in the diagnostic process was discussed in detail, emphasizing how advanced algorithms can support precise phenotypic assessment and patient health evaluation and contribute to the optimization of their treatment. Despite its great potential, the use of AI in the diagnosis of rare diseases is associated with challenges such as the need to standardize small patient groups and the necessity of interdisciplinary collaboration between experts in genetics, bioinformatics, laboratory medicine, and clinical medicine.
Modern approaches to the diagnosis of alpha-tryptasemia.
Zofia LM, Joanna L
J Appl Genet · 2026 Apr · PMID 42029822 · Publisher ↗
The purpose of the study was to determine the effectiveness of existing approaches to detect hereditary alpha-tryptasemia (HαT) and to identify key factors that affect the accuracy of differentiating this condition from...
The purpose of the study was to determine the effectiveness of existing approaches to detect hereditary alpha-tryptasemia (HαT) and to identify key factors that affect the accuracy of differentiating this condition from other disorders associated with elevated tryptase levels. Methodologically, the work was based on a systematic literature review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology, which involved critical analysis, selection, and synthesis of 62 scientific publications from 2019 to 2024, selected according to the criteria of availability of quantitative data on tryptase levels, genetic testing results and clinical symptoms. The results indicate that an increase in the number of copies of the TPSAB1 gene can be detected in 4–6% of the population and causes a consistently elevated basal tryptase level, which is associated with both an asymptomatic course (in approximately two-thirds of patients) and pathological manifestations such as gastrointestinal disorders, anaphylaxis, and neurovegetative disorders. It was found that the determination of “background” tryptase in the dynamics allows distinguishing hereditary elevation from acute mast cell degranulation, and a comprehensive genetic study of TPSAB1 together with the measurement of histamine, leukotrienes and prostaglandins increases the specificity of diagnosis. An important finding was that dysbiosis and related changes in intestinal barrier function can increase tryptase release and exacerbate clinical symptoms, which should be taken into account when choosing a therapeutic strategy. Given the data obtained, it was concluded that a multidisciplinary approach involving allergists, immunologists, and geneticists is needed, as well as periodic monitoring of tryptase levels. The practical significance lies in the improvement of diagnostic algorithms, which allows for earlier identification of hereditary alpha-tryptasemia and personalised management of patients.
Molecular interplay of lncRNAs, miRNAs, and mRNAs axes in triple-negative breast cancer: implications for metastatic progression.
Rathore D, Agarwal I, Patel S … +4 more , Adnani N, Dharwal N, Shukla N, Dave HV
J Appl Genet · 2026 Apr · PMID 42020663 · Publisher ↗
Triple-negative breast cancer (TNBC) constitutes 15-17% of all breast cancer cases. The absence of molecular targets restricts targeted therapy options for TNBC. Despite the availability of conventional chemotherapy, hig...
Triple-negative breast cancer (TNBC) constitutes 15-17% of all breast cancer cases. The absence of molecular targets restricts targeted therapy options for TNBC. Despite the availability of conventional chemotherapy, high recurrence rates and metastasis remain the primary challenges in current disease management. Nearly 46% of TNBC cases are metastasized to distant organs, which decreases the overall survival of TNBC patients. Therefore, identifying disease-specific markers, their mechanisms in metastasis, and their therapeutic potential could aid in developing better treatment options for patients. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs (> 200 nucleotides), exhibit significant function in gene expression regulation and tumorigenesis. LncRNAs play a significant role in TNBC metastasis through diverse mechanisms. LncRNAs such as H19, MALAT1, and others contribute to TNBC chemotherapy resistance, invasion, migration, relapse, and immune suppression. Furthermore, the molecular interactions among lncRNAs, miRNAs, and mRNAs collectively drive key hallmarks of metastatic progression, specifically in TNBC. To provide a comprehensive understanding of these mechanisms, this review highlights the biogenesis, classification, and physiological functions of lncRNAs, along with an overview of the metastatic cascade. Specifically, it emphasizes the regulatory axes of lncRNAs with miRNAs and mRNAs in driving metastatic progression, and explores their emerging role as promising biomarkers for diagnosis and targeted therapy. Expanding the understanding of lncRNA-mediated regulatory interactions could pave the way for the identification of novel biomarkers and the development of more effective therapeutic strategies to enhance TNBC diagnosis, prognosis, and treatment outcomes.
A novel engineered vector for TA cloning of PCR products.
Samiei A, Najafabadi ZH, Akbari N … +2 more , Khanahmad H, Mohammadi Farsani T
J Appl Genet · 2026 Apr · PMID 42002697 · Publisher ↗
INTRODUCTION: Optimized vectors are crucial in modern molecular biology because they greatly enhance the efficiency of the DNA cloning procedure. This study aimed to design a novel engineered vector containing an HphI ca...
INTRODUCTION: Optimized vectors are crucial in modern molecular biology because they greatly enhance the efficiency of the DNA cloning procedure. This study aimed to design a novel engineered vector containing an HphI cassette to enhance TA cloning efficiency. METHODS: The pTZ57R/T plasmid served as the basis for developing the novel Engineered vector (pTZ57R/T-2000). Three restriction sites (respectively, XbaI- HphI -SalI) were inserted into amplified fragments by specific primers. The PCR amplified fragments (1,000 bp) were digested by XbaI and SalI enzymes, then ligated into the modified pTZ57R/T plasmid (pTZ57R/T-HphI), which had been prepared by digestion with the same enzymes. Finally, the transformation and cloning efficiencies of the PCR products were assessed through the number of clones and colony PCR, respectively. RESULTS: The statistical analyses showed a significant difference in transformation efficiency between pTZ57R/T-2000 and ddT-tailed vectors (P < 0.0001), with the pTZ57R/T-2000 vector producing an average of 54 clones compared to 26.67 clones for the ddT-tailed vectors. However, there was no significant difference in TA cloning efficiency between the two vectors (P = 0.1069). DISCUSSION: The success rate of pTZ57R/T-2000 vector transformation is higher than ddT-tailed vector in terms of the number of clones. However, the TA cloning efficiency is lower in pTZ57R/T-2000 vectors compared to ddT-tailed vectors, to eliminate the assumption of a shortage of genes for cloning. To enhance the pTZ57R/T-2000 efficiency, it is recommended to use pre-divided tubes to reduce T-head damage during defreezing and pipetting.
From gametocides to gene drive: natural transmission distortion systems as tools for cereal breeding.
Kwiatek MT
J Appl Genet · 2026 Apr · PMID 41998473 · Publisher ↗
Natural segregation distortion systems are an important yet frequently overlooked component of genome dynamics in plants. Chromosomes carrying gametocidal genes (Gc), originating from Aegilops species, represent one of t...
Natural segregation distortion systems are an important yet frequently overlooked component of genome dynamics in plants. Chromosomes carrying gametocidal genes (Gc), originating from Aegilops species, represent one of the most widely studied chromosome-drive elements in cereals. By inducing chromosomal breakage in gametes that lack these genes and protecting those that inherit them, such chromosomes achieve strong preferential transmission, substantially affecting chromosome behavior in interspecific hybrids. Recent studies have revealed that, in wheat and triticale breeding, Gc systems can be used to stabilize alien chromatin and to secure the efficient introgression of resistance genes such as Lr32, Lr22, Lr39, Lr41, Pm13, Lr54, and Yr37. Their biased transmission can further support the maintenance of beneficial alleles or favorable allelic combinations within breeding populations. The activity of chromosomes bearing gametocidal genes facilitates the development of addition and substitution lines, promotes targeted chromosome rearrangements, and increases the retention of alien segments across backcross generations. The emergence of new genomic techniques has renewed interest in natural drive systems, and although homing-based drives remain limited in crops, chromosomes carrying Gc genes already provide a biologically contained and reliable mechanism of biased inheritance in polyploid cereals. This review summarizes the evolutionary and cytogenetic basis of Gc systems and highlights their relevance and future potential in chromosome engineering and cereal improvement.
Correction to: Discovery of core genes and intercellular communication role in osteosarcoma.
Meng F, Zhou X, Zhao Z … +2 more , Pei L, Xia W
J Appl Genet · 2026 Apr · PMID 41996024 · Publisher ↗
Abstract loading — click title to view on PubMed.
DDX11-AS1 regulates cell cycle signaling pathway and promotes proliferation and migration of lung adenocarcinoma by sponging miR-30a-5p and targeting CCNA2.
Xu C, Ai B
J Appl Genet · 2026 Apr · PMID 41996023 · Publisher ↗
Various long noncoding RNAs (lncRNAs) have a crucial part in treating lung adenocarcinoma (LUAD). However, there are few studies on lncRNA DDX11-AS1 in LUAD. We systematically elucidated its potential molecular mechanism...
Various long noncoding RNAs (lncRNAs) have a crucial part in treating lung adenocarcinoma (LUAD). However, there are few studies on lncRNA DDX11-AS1 in LUAD. We systematically elucidated its potential molecular mechanism in LUAD, which provides a theoretical basis for studying targeted therapy for LUAD. We have analyzed RNA expression in LUAD through TCGA-LUAD data. The binding site (…CAAAUGU…) was predicted by TargetScan database. Associated pathways were predicted by GSEA database. RT-qPCR to analyze RNA level and western blot to analyze protein abundance. Besides, CCK-8, EdU, Transwell and flow cytometry assays were performed to verify how DDX11-AS1, miR-30a-5p and CCNA2 affected LUAD cells. Targeted relationship was verified by dual luciferase reporter and RIP assays. The role of DDX11-AS1 in vivo was tested by a mouse model and immunohistochemistry. Compared with normal lung tissues or cells, LUAD tissues or cells had higher DDX11-AS1 expression and CCNA2 but lower miR-30a-5p expression. Proliferative, invasive and migratory abilities of LUAD cells could be enhanced by DDX11-AS1, which could further regulate cell cycle changes and attenuate apoptosis. MiR-30a-5p could be targeted and down-regulated by DDX11-AS1, which activated cell cycle signaling pathway through miR-30a-5p/CCNA2 axis. DDX11-AS1 promoted tumor growth in mice. Our research demonstrates that DDX11-AS1, through miR-30a-5p/CCNA2 axis, has a cancer-promotive part in LUAD development. It is suggested that DDX11-AS1 may be a new biomarker and therapeutic target in diagnosing and treating LUAD.
Effect of founder breeds on genotype imputation accuracy in Canchim cattle.
Teixeira R, Genuíno MVH, de Oliveira Bessa AF … +11 more , Dos Santos Câmara GM, de Jesus Oliveira AC, de Vasconcelos Silva JAI, Mota LFM, Baldi F, de Almeida Regitano LC, Marcondes CR, Bernardes PA, Berry DP, Munari DP, Buzanskas ME
J Appl Genet · 2026 Apr · PMID 41989735 · Publisher ↗
Genotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate wheth...
Genotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate whether the inclusion of genotypes from the founder breeds Nelore (NE) and Charolais (CH) improves the imputation accuracy in the composite beef cattle breed Canchim (CA). The populations studied consisted of 804 NE, 897 CH, and 392 CA animals, all genotyped using high-density panels (777,962 SNP – single nucleotide polymorphisms). CA animals had their genotypes masked to simulate a medium-density panel (54,609 SNP). Fourteen imputation scenarios were evaluated, varying according to breed, sex, year of birth, and lineage. Imputation accuracy was determined based on the percentage of correctly imputed genotypes (PERC) and the squared Pearson’s correlation between observed and imputed genotypes (R2). PERC values ranged from 66.52% to 97.39% and R² from 0.6352 to 0.9780. The scenarios that included NE, CH, and CA (males or animals born before 2004) as the reference population for imputing CA females or CA animals born after 2004 showed the highest imputation accuracies. Therefore, the use of founder breeds in the reference population improves the accuracy of genotype imputation in CA cattle. The results indicate that a multibreed reference population, incorporating founder breeds, could provide a more robust and informative genetic basis for imputing composite cattle.
Molecular profiling of 35 Phacelia species using SCoT molecular markers and genome size estimation.
Jedrzejczyk I, Lojko A, Rewers M
J Appl Genet · 2026 Mar · PMID 41912828 · Publisher ↗
The genus Phacelia comprises numerous species with significant ecological, agricultural, and ornamental value. Despite its diversity, the genetic relationships and genome size variation within Phacelia have remained poor...
The genus Phacelia comprises numerous species with significant ecological, agricultural, and ornamental value. Despite its diversity, the genetic relationships and genome size variation within Phacelia have remained poorly characterized. In this study, the nuclear DNA content (genome size) of 40 accessions representing 35 Phacelia species was estimated using flow cytometry (FCM), and genetic diversity was assessed using Start Codon Targeted (SCoT) molecular markers. The 2C nuclear DNA content ranged from 1.00 pg (P. ciliata) to 3.61 pg (P. egena), with notable inter- and intra-specific variation observed. SCoT marker analysis generated clear and reproducible banding patterns, enabling the construction of a UPGMA dendrogram that resolved the accessions into distinct groups, largely consistent with morphological and taxonomic relationships. Some closely related taxa, such as P. capitata and P. brachyloba, exhibited both high genetic similarity and comparable genome sizes, while significant divergence was observed among others. Although several well-supported clades identified in the SCoT-based phylogeny corresponded closely to established sections and subsections, certain taxa traditionally classified together were found in separate branches, suggesting complex evolutionary histories and potential morphological convergence. The results demonstrate that combining SCoT markers and genome size estimation provides valuable insights into the genetic diversity and evolutionary relationships within Phacelia, underscoring the importance of integrative molecular approaches for taxonomic and conservation studies in this genus.
Identification of candidate regions associated with resistance to early blight in tomato (Solanum lycopersicum L.) using BSA-seq.
Yessimseitova A, Nurtaza A, Tokbergenova Z … +3 more , Abdullaeva B, Dyussembekova D, Kakimzhanova A
J Appl Genet · 2026 Mar · PMID 41906061 · Publisher ↗
Early blight, caused by Alternaria alternata, is a key factor that reduces tomato yield and tomato product quality. Owing to the quantitative nature of resistance and the limited number of characterized loci, identificat...
Early blight, caused by Alternaria alternata, is a key factor that reduces tomato yield and tomato product quality. Owing to the quantitative nature of resistance and the limited number of characterized loci, identification of genomic regions associated with resistance remains an urgent task for breeding programs. Here, bulked segregant analysis with whole-genome resequencing (BSA-Seq) was used to identify candidate regions for resistance to early blight in the F₂ population obtained by crossing a resistant line (Gloria×BSS335) and a susceptible cultivar (Samaladay). A total of 14 overlapping candidate genomic regions were identified on chromosome 2 by intersecting SNP- and InDel-associated regions (totaling 0.26 Mb). Functional annotation of the 33 genes in this locus revealed the involvement of membrane proteins, components of signaling pathways, transcriptional regulators, and Rab GTPase family proteins, which are potentially involved in stress and immune responses. This is the first genome-wide study of early blight resistance in tomato in Kazakhstan. These results expand our understanding of the genetic architecture of early blight resistance and may serve as a basis for the functional validation of key candidate genes and their application in marker-assisted selection (MAS).
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